Awesome
CODEX-nf
Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX
Prerequisites
- R with package CODEX
- Rscript
and the following files:
- a bed file with the positions to consider
- a folder with Normal BAM files
- a folder with Tumor BAM files
Usage
nextflow run iarcbioinfo/CODEX-nf --dirNormal Normal --dirTumor Tumor --bedFile positions.bed --outdir output
Output
A series of files projectname_chromosome_optK_mode.txt, where chromosome takes its values in [1,2,...,22,X,Y], while projectname, optK, and mode are the same for all files. projectname and mode are specified by the user with options --project and --mode, respectively, and optK is computed by package CODEX.
All parameters
| PARAMETER | DEFAULT | DESCRIPTION |
|---|---|---|
| --help | null | Print usage and parameters |
| --dirNormal | Normal | Path to Normal BAM files |
| --dirTumor | Tumor | Path to Tumor BAM files |
| --outdir | . | Path to output directiry |
| --bedFile | positions.bed | Path to bed file with positions to consider |
| --rem_from_bed | _random|chrUn|GL000209R|GL000191R|GL000194R | Strings to exclude from the bed file chromosome list |
| --project | Project name | |
| --mem | 5 | Memory requested |
| --cpus | 1 | CPUs requested |
| --seg_mode | fraction | Mode for the segmentation algorithm (fraction or integer) |